[English] 日本語
Yorodumi
- PDB-5cdv: Proline dipeptidase from Deinococcus radiodurans R1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cdv
TitleProline dipeptidase from Deinococcus radiodurans R1
ComponentsProline dipeptidaseX-Pro dipeptidase
KeywordsHYDROLASE / xaa-Pro peptidase / prolidase / Deinococcus radiodurans
Function / homology
Function and homology information


metalloexopeptidase activity / transition metal ion binding / aminopeptidase activity
Similarity search - Function
Creatinase, N-terminal / Creatinase/Prolidase N-terminal domain / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily ...Creatinase, N-terminal / Creatinase/Prolidase N-terminal domain / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Proline dipeptidase
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsKumar, A. / Are, V. / Ghosh, B. / Jamdar, S. / Makde, R.
CitationJournal: To Be Published
Title: Proline dipeptidase from Deinococcus radiodurans R1 at 1.45 Angstrom resolution
Authors: Kumar, A. / Are, V. / Ghosh, B. / Jamdar, S. / Makde, R.
History
DepositionJul 5, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proline dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7008
Polymers37,1471
Non-polymers5537
Water6,684371
1
A: Proline dipeptidase
hetero molecules

A: Proline dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,39916
Polymers74,2932
Non-polymers1,10614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4730 Å2
ΔGint-91 kcal/mol
Surface area27810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.619, 60.619, 202.784
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-851-

HOH

-
Components

#1: Protein Proline dipeptidase / X-Pro dipeptidase


Mass: 37146.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: DR_1246 / Plasmid: pST50Tr / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q9RUY4
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 5
Details: 0.1M HEPES pH 7.5, 0.8M NaH2PO4, 0.8M KH2PO4, 10mM Tris-Cl pH 8.0, 100mM NaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 8, 2013
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.45→39.48 Å / Num. obs: 67571 / % possible obs: 99.1 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 24.5
Reflection shellResolution: 1.45→1.45 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 5.7 / % possible all: 90.3

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Cootmodel building
PHENIXmodel building
PHASERphasing
Aimlessdata scaling
XDSdata processing
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q6D

3q6d


Resolution: 1.45→39.48 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1978 3366 4.99 %Random
Rwork0.1817 ---
obs0.1825 67444 98.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→39.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2592 0 27 371 2990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092662
X-RAY DIFFRACTIONf_angle_d1.2913622
X-RAY DIFFRACTIONf_dihedral_angle_d11.916969
X-RAY DIFFRACTIONf_chiral_restr0.047416
X-RAY DIFFRACTIONf_plane_restr0.006477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.47070.21911250.21052365X-RAY DIFFRACTION89
1.4707-1.49270.27761050.222494X-RAY DIFFRACTION94
1.4927-1.5160.20531140.18112605X-RAY DIFFRACTION96
1.516-1.54090.23071490.1782617X-RAY DIFFRACTION100
1.5409-1.56740.18841660.17012611X-RAY DIFFRACTION100
1.5674-1.59590.18271400.16932700X-RAY DIFFRACTION100
1.5959-1.62660.18111250.17162628X-RAY DIFFRACTION100
1.6266-1.65980.20411440.16122662X-RAY DIFFRACTION100
1.6598-1.69590.19681410.16462667X-RAY DIFFRACTION100
1.6959-1.73540.20891620.17072669X-RAY DIFFRACTION100
1.7354-1.77880.17881440.16422647X-RAY DIFFRACTION100
1.7788-1.82690.19591320.16742666X-RAY DIFFRACTION100
1.8269-1.88060.19461290.17622684X-RAY DIFFRACTION100
1.8806-1.94130.2641230.26742673X-RAY DIFFRACTION99
1.9413-2.01070.18881460.1812666X-RAY DIFFRACTION100
2.0107-2.09120.18351480.17342692X-RAY DIFFRACTION99
2.0912-2.18640.17951200.16542694X-RAY DIFFRACTION100
2.1864-2.30160.25871460.23822677X-RAY DIFFRACTION99
2.3016-2.44580.18481550.1862699X-RAY DIFFRACTION100
2.4458-2.63460.20091630.1772704X-RAY DIFFRACTION100
2.6346-2.89970.21011590.18672730X-RAY DIFFRACTION100
2.8997-3.31910.19831390.17922768X-RAY DIFFRACTION100
3.3191-4.1810.1711420.15912801X-RAY DIFFRACTION100
4.181-39.49560.1741490.17222959X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.34330.17860.48620.22150.23150.49760.08240.0497-0.05150.07070.0161-0.05550.09070.01160.07530.07450.008-0.01720.0737-0.00290.08874.84-16.9141-0.6354
20.34140.048-0.38630.03690.210.40320.00190.14230.02750.0793-0.0046-0.0385-0.0181-0.15320.00690.04880.0249-0.00240.13210.0160.0893-27.4777-26.701-12.2493
30.14550.384-0.28170.0352-0.40.9092-0.00440.10960.04890.00130.1257-0.0062-0.1591-0.16330.07280.06240.0335-0.00590.11910.01540.0761-17.8616-20.3075-26.3209
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 128 )
2X-RAY DIFFRACTION2chain 'A' and (resid 129 through 232 )
3X-RAY DIFFRACTION3chain 'A' and (resid 233 through 349 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more